I've seen this with other ships (including
ships), but it's always just been fine for me until now, and I've never bothered to learn how it works.
I just downloaded the Dysnomia dump to grab the Sizifus/Quirinus freighter. I made minimal modifications to the tbl - removing non-FS weapons in the turrets, fixing the double "engine02" entry - and plopped it and its two cargo containers in FRED. However, the cargo containers can only dock with the "top dock" on the Quirinus, and not the two actual cargo bays.
I might just get rid of it and use the Triton because tbh I probably just have I-want-too-many-custom-ships syndrome, but I am curious: what causes this? How would I fix it?